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<p>The PDB archive is now including annotation of protein chemical modifications (PCMs) and post-translational modifications (PTMs) in a standardized way.</p>

<p><a href="https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2024*662fa1a565d8a8cacaf76f9c__;Iw!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGuW0h1_x$">As previously announced</a>, the <a href="https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGh6Zu0C0$">PDBx/mmCIF dictionary</a> has been extended to enhance PCM and PTM annotation.</p>

<p>This includes new PDBx/mmCIF categories and items as follows:</p>

<p>In the Chemical Component Definition (CCD) files:</p>

<ul>

<li>A new item in the <a href="https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/chem_comp.html__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGttIPrUO$">chem_comp</a> category: <a href="https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_pcm.html__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGvrnfA1y$">chem_comp.pdbx_pcm</a>, stating whether the CCD is a known PCM/PTM.</li>

<li>A new category called <a href="https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_chem_comp_pcm.html__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGlcrj8Pq$">pdbx_chem_comp_pcm</a>, stating the PCM/PTM <a href="https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_chem_comp_pcm.type.html__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGs6_-Qmo$">type</a> and <a href="https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_chem_comp_pcm.category.html__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGnX8skkH$">category</a>, as well as on which positions in the amino acid and in the polypeptide it is expected to be observed. If this PCM is also a known PTM, it will have the Uniprot PTM accession ID.</li>

</ul>

<p>In the atomic coordinate files:</p>

<ul>

<li>A new item in the <a href="https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_entry_details.html__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGt5TBZKp$">pdbx_entry_details</a> category: <a href="https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_entry_details.has_protein_modification.html__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGixjrnQh$">pdbx_entry_details.has_protein_modification</a>, stating if the entry contains a PCM/PTM.</li>

<li>A new category called <a href="https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_modification_feature.html__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGkbbaPQp$">pdbx_modification_feature</a>, providing an instance-level annotation of all observed PCMs/PTMs within the entry, as well as their type and category.</li>

</ul>

<p>Additionally to providing this new annotation, any protein modifications that are inconsistently handled within PDB entries are amended, to ensure that a given modification is consistently handled in the PDB archive. This includes a major clean-up of incorrect link records (struct_conn).</p>

<p>All entries containing protein modifications are being re-released gradually from October 2024, throughout Spring 2025.</p>

<p>This standardization ensures that there is a single approach to handling each protein modification that occurs within the PDB archive, allowing better findability.</p>

<p>Questions or feedback? Contact <a href="mailto:deposit-help@mail.wwpdb.org">deposit-help@mail.wwpdb.org</a>.</p>

<p>The protein chemical modifications (PCMs) and post translational modifications (PTMs) remediation project is a wwPDB collaborative project carried out principally by <a href="https://urldefense.com/v3/__https://www.ebi.ac.uk/pdbe/__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGtnysGZ6$">PDBe</a> at <a href="https://urldefense.com/v3/__https://www.ebi.ac.uk/__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGoOnKg4G$">EMBL-EBI</a>, and is funded by BBSRC grant number BB/V018779/1.</p>


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